Is ABCC9 p.Leu1089= (c.3267G>A) pathogenic?

ABCC9 p.Leu1089= (c.3267G>A) is classified Benign in ABCC9 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-03). Rare (popmax 0.103%, eas); Associated with dilated cardiomyopathy 1O.

What condition is associated with ABCC9 p.Leu1089= (c.3267G>A)?

ABCC9 p.Leu1089= (c.3267G>A) is associated with dilated cardiomyopathy 1O (ClinVar).

How common is ABCC9 p.Leu1089= (c.3267G>A) in the general population?

ABCC9 p.Leu1089= (c.3267G>A) is rare (popmax 0.103%, eas) (gnomAD).

How is Familial isolated dilated cardiomyopathy inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ABCC9 p.Leu1089=

c.3267G>A · rs780998911 · VCV416406

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.103%, eas)

Conditions

dilated cardiomyopathy 1O

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.51	GERP -3.1, phastCons 0.026
Overall
CADD	5.021	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.103% East Asian · 46/44,856 alleles

Filtering AF 0.079% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0707%

Overall 0.00291% 47/1,613,500 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.103%	975
Remaining individualsnot grpmax-eligible	0.0016%	62,464

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ABCC9
Protein: p.Leu1089=
Coding: c.3267G>A
MANE Select: NM_020297
dbSNP: rs780998911
Type: single nucleotide variant
Location: chr12:21844531 (GRCh38)
Gene constraint: LOEUF 0.557 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.72
Residue 1089: the abc transmembrane type-1 2 domain

Full ABCC9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

dilated cardiomyopathy 1O — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Familial isolated dilated cardiomyopathy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: All ages
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

ABCC9 p.Leu1089Gln Uncertain significance ★ ⚠ same residue
ABCC9 p.Leu1089Val Uncertain significance ★ ⚠ same residue
ABCC9 c.2506-1G>A Pathogenic/Likely pathogenic ★★ same condition
ABCC9 p.Arg1116Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
ABCC9 p.Arg1116His Pathogenic ★★ ⚠ same condition
ABCC9 p.Arg1154Gln Pathogenic ★★ same condition
ABCC9 p.Arg1154Trp Pathogenic/Likely pathogenic ★★ same condition
ABCC9 p.Gln852Ter Pathogenic/Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/abcc9-p-leu1089 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown